Semiconductor quantum dots (QDs) are thought to be the most promising fluorescent probe for biological and biomedical applications because of their unique size-dependent optical and electronic properties. QD bioconjugates provide important advantages over conventional organic dyes. This review compares the optical properties of nanoparticles and dyes and describes the surface modification of the QDs and the methods for biomolecules conjugating to QDs. In addition, the effect of QDs on normal physiology in real biological applications is discussed.